Human immunodeficiency virus (“HIV”) is a member of the genus Lentivirinae, which is part of the family of Retroviridae. Lentiviruses are transmitted as single-stranded, positive-sense, enveloped RNA viruses. Upon entry of the target cell, the viral RNA genome is converted to double-stranded DNA by a virally encoded reverse transcriptase. This viral DNA then is integrated into the cellular DNA by a virally encoded integrase, along with host cellular co-factors, so that the viral genome can be transcribed. After the virus has infected the cell, two pathways are possible: (1) the virus becomes latent and the infected cell continues to function, or (2) the virus becomes active and replicates.
There are two strains of HIV known to exist: HIV-1 and HIV-2.
In HIV-1, the HIV-1 protease is synthesized as part of a 165 kDa polyprotein (Gag-Pol). Gag-Pol comprises the matrix, capsid, P2, nucleocapsid, transframe, protease (PR), reverse transcriptase, and integrase domains. The protease mediates its own release and the processing of the viral polyproteins, Gag, and Gag-Pol, into the necessary structural and functional proteins. This spatio-temporally regulated process is crucial for the maturation and propagation of HIV.
The HIV-1 protease is composed of 99 amino acids and is a member of the family of aspartic acid proteases. Unlike the cellular aspartic proteases that are active as monomers, catalytic activity of retroviral proteases, including HIV-1 proteases, requires dimer formation. All aspartic proteases, including retroviral proteases, share the triplet DTG (Asp25, Thr26 and Gly27) critical for the active site geometry and catalytic function. These residues interact closely in the active, dimeric structure of HIV-1 proteases. The active site is formed along the dimer interface, and each subunit contributes one of the two catalytic aspartic acid residues. These residues are expected to be in opposite states of protonation for activity, and the water molecule involved in the hydrolysis of the peptide bond has been proposed to be hydrogen bonded to the aspartyl residues. The hydrolysis of the peptide bond mediated by the protease involves general base/general acid catalysis. Additionally, studies of the steps in the maturation of the Gag-Pol precursor and the mechanism of the autocatalytic maturation of the protease have revealed that upon its intramolecular maturation at its N-terminus, the protease forms a stable dimer concomitant with the formation of the terminal β-sheet structure and a very low equilibrium dimer dissociation constant (Kd<10 nM).
HIV protease inhibitors (“HIV-PIs”), which are designed to inhibit the HIV aspartyl protease, are key components of highly active antiretroviral therapy (“HAART”), but they have been associated with adverse side effects, including partial lipodystrophy and metabolic syndrome. The emergence of drug-resistant HIV proteases has coincided with the widespread use of HIV-PIs. In these drug-resistant HIV proteases, mutations have been found in at least 49 of the 99 amino acids of the coding sequence. The loss of responsiveness to HIV-PI treatment has been directly correlated to substitutions at 18 or more positions. Hence, there is a need for new HIV-PIs.